Starting phenix.real_space_refine
on Fri Oct 10 13:20:19 2025 by dcliebschner
===============================================================================

Processing files:
-------------------------------------------------------------------------------

  Found model, /net/cci-nas-00/data/ceres_data/8rao_19021/10_2025/8rao_19021.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rao_19021/10_2025/8rao_19021.map

Processing PHIL parameters:
-------------------------------------------------------------------------------

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rao_19021/10_2025/8rao_19021.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rao_19021/10_2025/8rao_19021.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rao_19021/10_2025/8rao_19021.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rao_19021/10_2025/8rao_19021.cif"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 8
    Type Number    sf(0)   Gaussians
     P      11      5.49       5
     Mg      1      5.21       5
     S      31      5.16       5
     Be      1      3.05       5
     C    3604      2.51       5
     N    1010      2.21       5
     O    1120      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 31 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5781
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "O"
      Number of atoms: 5557
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 694, 5557
          Classifications: {'peptide': 694}
          Link IDs: {'PTRANS': 28, 'TRANS': 665}
          Chain breaks: 2
    Chain: "P"
      Number of atoms: 192
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 192
          Classifications: {'RNA': 9}
          Modifications used: {'rna2p_pur': 3, 'rna2p_pyr': 2, 'rna3p_pur': 1, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 4, 'rna3p': 4}
    Chain: "O"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 32
          Unusual residues: {' MG': 1, 'ADP': 1, 'BEF': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 1.34, per 1000 atoms: 0.23
  Number of scatterers: 5781
  At special positions: 0
  Unit cell: (77.7, 102.9, 96.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 8
    Type Number    sf(0)
     S      31     16.00
     P      11     15.00
     Mg      1     11.99
     F       3      9.00
     O    1120      8.00
     N    1010      7.00
     C    3604      6.00
     Be      1      4.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.63
  Conformation dependent library (CDL) restraints added in 272.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1312

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 4 sheets defined
      52.9% alpha, 15.6% beta
      0 base pairs and 2 stacking pairs defined.
    Time for finding SS restraints: 0.57
  Creating SS restraints...
    Processing helix  chain 'O' and resid 1095 through 1110
    Processing helix  chain 'O' and resid 1113 through 1121
    Processing helix  chain 'O' and resid 1136 through 1140
    Processing helix  chain 'O' and resid 1149 through 1175
      Proline residue:  O1159  - end of helix
    Processing helix  chain 'O' and resid 1203 through 1210
    Processing helix  chain 'O' and resid 1232 through 1239
      removed outlier: 3.629A  pdb=" N   PHE O1236 " --> pdb=" O   SER O1232 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1268 through 1274
    Processing helix  chain 'O' and resid 1288 through 1301
    Processing helix  chain 'O' and resid 1302 through 1305
      removed outlier: 6.161A  pdb=" N   ASP O1305 " --> pdb=" O   GLU O1302 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 1302 through 1305'
    Processing helix  chain 'O' and resid 1306 through 1313
    Processing helix  chain 'O' and resid 1322 through 1334
      removed outlier: 3.616A  pdb=" N   ILE O1326 " --> pdb=" O   ASP O1322 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1336 through 1349
    Processing helix  chain 'O' and resid 1362 through 1377
    Processing helix  chain 'O' and resid 1412 through 1425
      removed outlier: 3.617A  pdb=" N   SER O1425 " --> pdb=" O   LEU O1421 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1452 through 1455
    Processing helix  chain 'O' and resid 1456 through 1465
    Processing helix  chain 'O' and resid 1531 through 1562
    Processing helix  chain 'O' and resid 1570 through 1573
      removed outlier: 3.702A  pdb=" N   ALA O1573 " --> pdb=" O   SER O1570 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 1570 through 1573'
    Processing helix  chain 'O' and resid 1574 through 1581
    Processing helix  chain 'O' and resid 1592 through 1595
      removed outlier: 3.589A  pdb=" N   CYS O1595 " --> pdb=" O   ALA O1592 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 1592 through 1595'
    Processing helix  chain 'O' and resid 1596 through 1602
    Processing helix  chain 'O' and resid 1603 through 1606
      removed outlier: 3.819A  pdb=" N   TYR O1606 " --> pdb=" O   PRO O1603 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 1603 through 1606'
    Processing helix  chain 'O' and resid 1626 through 1632
    Processing helix  chain 'O' and resid 1637 through 1646
    Processing helix  chain 'O' and resid 1658 through 1669
      removed outlier: 4.550A  pdb=" N   PHE O1664 " --> pdb=" O   SER O1660 " (cutoff:3.500A)
      Proline residue:  O1665  - end of helix
    Processing helix  chain 'O' and resid 1679 through 1684
    Processing helix  chain 'O' and resid 1686 through 1691
      removed outlier: 4.041A  pdb=" N   GLN O1690 " --> pdb=" O   ARG O1686 " (cutoff:3.500A)
      removed outlier: 4.222A  pdb=" N   LEU O1691 " --> pdb=" O   PRO O1687 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'O' and resid 1686 through 1691'
    Processing helix  chain 'O' and resid 1718 through 1737
      removed outlier: 3.955A  pdb=" N   ILE O1722 " --> pdb=" O   ASN O1718 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1752 through 1767
    Processing helix  chain 'O' and resid 1769 through 1774
      removed outlier: 3.996A  pdb=" N   LYS O1773 " --> pdb=" O   GLY O1769 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1805 through 1809
      removed outlier: 3.873A  pdb=" N   LEU O1808 " --> pdb=" O   VAL O1805 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1810 through 1819
      removed outlier: 3.606A  pdb=" N   MET O1814 " --> pdb=" O   ASP O1810 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1830 through 1836
      removed outlier: 3.871A  pdb=" N   LYS O1836 " --> pdb=" O   ARG O1832 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 1837 through 1850
    Processing helix  chain 'O' and resid 1865 through 1876
      removed outlier: 3.783A  pdb=" N   GLN O1869 " --> pdb=" O   ASN O1865 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'O' and resid 1188 through 1191
      removed outlier: 3.655A  pdb=" N   ASN O1257 " --> pdb=" O   THR O1253 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   THR O1249 " --> pdb=" O   THR O1261 " (cutoff:3.500A)
      removed outlier: 6.782A  pdb=" N   ARG O1263 " --> pdb=" O   VAL O1247 " (cutoff:3.500A)
      removed outlier: 5.776A  pdb=" N   VAL O1247 " --> pdb=" O   ARG O1263 " (cutoff:3.500A)
      removed outlier: 8.635A  pdb=" N   HIS O1265 " --> pdb=" O   ALA O1245 " (cutoff:3.500A)
      removed outlier: 8.886A  pdb=" N   ALA O1245 " --> pdb=" O   HIS O1265 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ASP O1215 " --> pdb=" O   VAL O1247 " (cutoff:3.500A)
      removed outlier: 7.114A  pdb=" N   LEU O1216 " --> pdb=" O   VAL O1285 " (cutoff:3.500A)
      removed outlier: 8.867A  pdb=" N   SER O1182 " --> pdb=" O   ALA O1202 " (cutoff:3.500A)
      removed outlier: 5.970A  pdb=" N   ALA O1202 " --> pdb=" O   SER O1182 " (cutoff:3.500A)
      removed outlier: 3.963A  pdb=" N   ILE O1184 " --> pdb=" O   SER O1200 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   SER O1200 " --> pdb=" O   ILE O1184 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'O' and resid 1439 through 1441
      removed outlier: 6.606A  pdb=" N   ILE O1406 " --> pdb=" O   ILE O1565 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   SER O1567 " --> pdb=" O   ILE O1406 " (cutoff:3.500A)
      removed outlier: 6.207A  pdb=" N   ILE O1408 " --> pdb=" O   SER O1567 " (cutoff:3.500A)
      removed outlier: 6.719A  pdb=" N   VAL O1587 " --> pdb=" O   ILE O1612 " (cutoff:3.500A)
      removed outlier: 7.941A  pdb=" N   VAL O1614 " --> pdb=" O   VAL O1587 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   ILE O1589 " --> pdb=" O   VAL O1614 " (cutoff:3.500A)
      removed outlier: 5.814A  pdb=" N   GLY O1351 " --> pdb=" O   CYS O1611 " (cutoff:3.500A)
      removed outlier: 7.275A  pdb=" N   MET O1613 " --> pdb=" O   GLY O1351 " (cutoff:3.500A)
      removed outlier: 6.282A  pdb=" N   SER O1353 " --> pdb=" O   MET O1613 " (cutoff:3.500A)
      removed outlier: 8.791A  pdb=" N   TYR O1649 " --> pdb=" O   PHE O1352 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   LEU O1354 " --> pdb=" O   TYR O1649 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'O' and resid 1427 through 1428
    Processing sheet with id=AA4, first strand: chain 'O' and resid 1775 through 1778
      removed outlier: 6.779A  pdb=" N   ILE O1746 " --> pdb=" O   ASP O1776 " (cutoff:3.500A)
      removed outlier: 8.180A  pdb=" N   ASN O1778 " --> pdb=" O   ILE O1746 " (cutoff:3.500A)
      removed outlier: 6.083A  pdb=" N   ILE O1748 " --> pdb=" O   ASN O1778 " (cutoff:3.500A)
      removed outlier: 6.813A  pdb=" N   GLY O1747 " --> pdb=" O   LEU O1792 " (cutoff:3.500A)
      removed outlier: 7.724A  pdb=" N   SER O1794 " --> pdb=" O   GLY O1747 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   ILE O1749 " --> pdb=" O   SER O1794 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   GLU O1789 " --> pdb=" O   SER O1824 " (cutoff:3.500A)
      removed outlier: 8.112A  pdb=" N   TRP O1826 " --> pdb=" O   GLU O1789 " (cutoff:3.500A)
      removed outlier: 6.549A  pdb=" N   ILE O1791 " --> pdb=" O   TRP O1826 " (cutoff:3.500A)
      removed outlier: 7.671A  pdb=" N   LEU O1828 " --> pdb=" O   ILE O1791 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   ILE O1793 " --> pdb=" O   LEU O1828 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   ALA O1854 " --> pdb=" O   TYR O1697 " (cutoff:3.500A)
      removed outlier: 5.938A  pdb=" N   PHE O1699 " --> pdb=" O   ALA O1854 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   ALA O1856 " --> pdb=" O   PHE O1699 " (cutoff:3.500A)
      removed outlier: 5.285A  pdb=" N   ASP O1701 " --> pdb=" O   ALA O1856 " (cutoff:3.500A)

    256 hydrogen bonds defined for protein.
    735 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      2 stacking parallelities
  Total time for adding SS restraints: 0.96

  Time building geometry restraints manager: 0.76 seconds

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.

  Histogram of bond lengths:
        1.22 -     1.34: 1854
        1.34 -     1.45: 742
        1.45 -     1.57: 3239
        1.57 -     1.69: 20
        1.69 -     1.81: 49
  Bond restraints: 5904
  Sorted by residual:
  bond pdb=" F2  BEF O3003 "
       pdb="BE   BEF O3003 "
    ideal  model  delta    sigma   weight residual
    1.476  1.562 -0.086 2.00e-02 2.50e+03 1.83e+01
  bond pdb=" F3  BEF O3003 "
       pdb="BE   BEF O3003 "
    ideal  model  delta    sigma   weight residual
    1.476  1.546 -0.070 2.00e-02 2.50e+03 1.22e+01
  bond pdb=" F1  BEF O3003 "
       pdb="BE   BEF O3003 "
    ideal  model  delta    sigma   weight residual
    1.476  1.534 -0.058 2.00e-02 2.50e+03 8.42e+00
  bond pdb=" C4  ADP O3001 "
       pdb=" C5  ADP O3001 "
    ideal  model  delta    sigma   weight residual
    1.490  1.470  0.020 2.00e-02 2.50e+03 1.02e+00
  bond pdb=" N1    C P   4 "
       pdb=" C2    C P   4 "
    ideal  model  delta    sigma   weight residual
    1.397  1.410 -0.013 2.00e-02 2.50e+03 3.96e-01
  ... (remaining 5899 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 7953
        2.52 -     5.04: 41
        5.04 -     7.55: 6
        7.55 -    10.07: 0
       10.07 -    12.59: 2
  Bond angle restraints: 8002
  Sorted by residual:
  angle pdb=" F2  BEF O3003 "
        pdb="BE   BEF O3003 "
        pdb=" F3  BEF O3003 "
      ideal   model   delta    sigma   weight residual
     119.96  107.37   12.59 3.00e+00 1.11e-01 1.76e+01
  angle pdb=" F1  BEF O3003 "
        pdb="BE   BEF O3003 "
        pdb=" F3  BEF O3003 "
      ideal   model   delta    sigma   weight residual
     120.12  110.03   10.09 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" F1  BEF O3003 "
        pdb="BE   BEF O3003 "
        pdb=" F2  BEF O3003 "
      ideal   model   delta    sigma   weight residual
     119.91  112.44    7.47 3.00e+00 1.11e-01 6.20e+00
  angle pdb=" C1'   C P   4 "
        pdb=" N1    C P   4 "
        pdb=" C2    C P   4 "
      ideal   model   delta    sigma   weight residual
     118.80  125.43   -6.63 3.00e+00 1.11e-01 4.88e+00
  angle pdb=" C2'   C P   4 "
        pdb=" C1'   C P   4 "
        pdb=" N1    C P   4 "
      ideal   model   delta    sigma   weight residual
     112.00  114.84   -2.84 1.50e+00 4.44e-01 3.58e+00
  ... (remaining 7997 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.90: 3556
       23.90 -    47.80: 57
       47.80 -    71.70: 26
       71.70 -    95.60: 4
       95.60 -   119.51: 2
  Dihedral angle restraints: 3645
    sinusoidal: 1614
      harmonic: 2031
  Sorted by residual:
  dihedral pdb=" O4'   C P   4 "
           pdb=" C1'   C P   4 "
           pdb=" N1    C P   4 "
           pdb=" C2    C P   4 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00  102.01   97.99     1      1.50e+01 4.44e-03 4.86e+01
  dihedral pdb=" O1B ADP O3001 "
           pdb=" O3A ADP O3001 "
           pdb=" PB  ADP O3001 "
           pdb=" PA  ADP O3001 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -179.51  119.51     1      2.00e+01 2.50e-03 3.58e+01
  dihedral pdb=" O5'   C P   8 "
           pdb=" C5'   C P   8 "
           pdb=" C4'   C P   8 "
           pdb=" C3'   C P   8 "
      ideal   model   delta sinusoidal    sigma   weight residual
      55.00  114.85  -59.85     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 3642 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.025: 587
       0.025 -    0.051: 180
       0.051 -    0.076: 45
       0.076 -    0.101: 40
       0.101 -    0.126: 35
  Chirality restraints: 887
  Sorted by residual:
  chirality pdb=" CA  ILE O1280 "
            pdb=" N   ILE O1280 "
            pdb=" C   ILE O1280 "
            pdb=" CB  ILE O1280 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.13 2.00e-01 2.50e+01 3.98e-01
  chirality pdb=" CA  ILE O1825 "
            pdb=" N   ILE O1825 "
            pdb=" C   ILE O1825 "
            pdb=" CB  ILE O1825 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.85e-01
  chirality pdb=" CA  ILE O1564 "
            pdb=" N   ILE O1564 "
            pdb=" C   ILE O1564 "
            pdb=" CB  ILE O1564 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.56   -0.12 2.00e-01 2.50e+01 3.83e-01
  ... (remaining 884 not shown)

  Planarity restraints: 997
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER O1647 "    0.018 5.00e-02 4.00e+02   2.66e-02 1.13e+00
        pdb=" N   PRO O1648 "   -0.046 5.00e-02 4.00e+02
        pdb=" CA  PRO O1648 "    0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO O1648 "    0.015 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU O1222 "   -0.014 5.00e-02 4.00e+02   2.19e-02 7.70e-01
        pdb=" N   PRO O1223 "    0.038 5.00e-02 4.00e+02
        pdb=" CA  PRO O1223 "   -0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO O1223 "   -0.012 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY O1357 "    0.013 5.00e-02 4.00e+02   1.97e-02 6.21e-01
        pdb=" N   PRO O1358 "   -0.034 5.00e-02 4.00e+02
        pdb=" CA  PRO O1358 "    0.010 5.00e-02 4.00e+02
        pdb=" CD  PRO O1358 "    0.011 5.00e-02 4.00e+02
  ... (remaining 994 not shown)

  Histogram of nonbonded interaction distances:
        2.02 -     2.59: 59
        2.59 -     3.17: 5264
        3.17 -     3.75: 9127
        3.75 -     4.32: 13028
        4.32 -     4.90: 21362
  Nonbonded interactions: 48840
  Sorted by model distance:
  nonbonded pdb=" OG1 THR O1364 "
            pdb="MG    MG O3002 "
     model   vdw
     2.016 2.170
  nonbonded pdb=" O2B ADP O3001 "
            pdb="MG    MG O3002 "
     model   vdw
     2.016 2.170
  nonbonded pdb=" OE2 GLU O1591 "
            pdb=" F1  BEF O3003 "
     model   vdw
     2.166 2.990
  nonbonded pdb=" O   TYR O1125 "
            pdb=" NH1 ARG O1173 "
     model   vdw
     2.167 3.120
  nonbonded pdb=" OG  SER O1332 "
            pdb=" O   LYS O1430 "
     model   vdw
     2.174 3.040
  ... (remaining 48835 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.310
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.310
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.100
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7822
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.086   5904  Z= 0.116
  Angle     :  0.462  12.589   8002  Z= 0.220
  Chirality :  0.038   0.126    887
  Planarity :  0.002   0.027    997
  Dihedral  : 10.681 119.506   2333
  Min Nonbonded Distance : 2.016

Molprobity Statistics.
  All-atom Clashscore : 4.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.60 %
    Favored  : 98.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.69 (0.34), residues: 688
  helix:  3.31 (0.31), residues: 333
  sheet:  0.87 (0.44), residues: 129
  loop : -0.05 (0.42), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG O1820 
 TYR   0.004   0.000   TYR O1195 
 PHE   0.006   0.001   PHE O1860 
 TRP   0.003   0.000   TRP O1688 
 HIS   0.002   0.000   HIS O1574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00222 ( 5904)
  covalent geometry    : angle       0.46201 ( 8002)
  hydrogen bonds       : bond        0.13236 (  256)
  hydrogen bonds       : angle       4.24797 (  735)

*********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.244 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9440 (tpt) cc_final: 0.9047 (tpt)
REVERT: O 1157 MET cc_start: 0.9183 (mmm) cc_final: 0.8705 (mmm)
REVERT: O 1162 LEU cc_start: 0.9747 (mt) cc_final: 0.9500 (pp)
REVERT: O 1294 GLU cc_start: 0.9405 (mt-10) cc_final: 0.9175 (mt-10)
REVERT: O 1439 LEU cc_start: 0.6606 (tp) cc_final: 0.4436 (tp)
REVERT: O 1566 CYS cc_start: 0.9572 (m) cc_final: 0.9255 (p)
REVERT: O 1582 ILE cc_start: 0.8955 (pt) cc_final: 0.7624 (pt)
REVERT: O 1584 PHE cc_start: 0.9071 (m-80) cc_final: 0.8682 (m-80)
REVERT: O 1613 MET cc_start: 0.9669 (mtm) cc_final: 0.9242 (mtp)
REVERT: O 1625 LEU cc_start: 0.9645 (mt) cc_final: 0.9440 (mm)
REVERT: O 1783 PHE cc_start: 0.9209 (t80) cc_final: 0.8629 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1100
  time to fit residues: 18.0363
Evaluate side-chains
  84 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 49 optimal weight:    6.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
O1139 ASN
O1555 GLN
O1757 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.050780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.036262 restraints weight = 39352.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.037579 restraints weight = 25203.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.2962 r_free = 0.2962 target = 0.038521 restraints weight = 18451.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.039132 restraints weight = 14744.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.039664 restraints weight = 12639.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.2954
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5904  Z= 0.130
  Angle     :  0.576   8.080   8002  Z= 0.282
  Chirality :  0.042   0.245    887
  Planarity :  0.004   0.047    997
  Dihedral  : 12.845 107.881    925
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.07 (0.33), residues: 688
  helix:  2.53 (0.30), residues: 338
  sheet:  0.68 (0.44), residues: 132
  loop :  0.01 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG O1820 
 TYR   0.013   0.001   TYR O1117 
 PHE   0.033   0.002   PHE O1763 
 TRP   0.011   0.002   TRP O1166 
 HIS   0.002   0.001   HIS O1574 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 5904)
  covalent geometry    : angle       0.57616 ( 8002)
  hydrogen bonds       : bond        0.03414 (  256)
  hydrogen bonds       : angle       4.31224 (  735)

*********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9325 (tpt) cc_final: 0.8872 (tpt)
REVERT: O 1157 MET cc_start: 0.8761 (mmm) cc_final: 0.8408 (mmm)
REVERT: O 1216 LEU cc_start: 0.8983 (tp) cc_final: 0.8764 (tt)
REVERT: O 1294 GLU cc_start: 0.9289 (mt-10) cc_final: 0.9070 (mt-10)
REVERT: O 1418 GLU cc_start: 0.8973 (tt0) cc_final: 0.8766 (mt-10)
REVERT: O 1566 CYS cc_start: 0.9494 (m) cc_final: 0.9239 (p)
REVERT: O 1584 PHE cc_start: 0.8722 (m-80) cc_final: 0.8378 (m-80)
REVERT: O 1613 MET cc_start: 0.9523 (mtm) cc_final: 0.8958 (mtp)
REVERT: O 1776 ASP cc_start: 0.8659 (t0) cc_final: 0.7933 (m-30)
REVERT: O 1783 PHE cc_start: 0.9011 (t80) cc_final: 0.8272 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 102
  average time/residue: 0.0973
  time to fit residues: 12.5099
Evaluate side-chains
  75 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 66 optimal weight:    1.9990
   chunk 2 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 40 optimal weight:    0.7980
   chunk 5 optimal weight:    3.9990
   chunk 67 optimal weight:    8.9990
   chunk 25 optimal weight:    0.9980
   chunk 14 optimal weight:    4.9990
   chunk 31 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
O1241 HIS
O1312 GLN
** O1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
O1831 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.049505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.035169 restraints weight = 39953.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.036412 restraints weight = 25639.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2924 r_free = 0.2924 target = 0.037287 restraints weight = 18867.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.2944 r_free = 0.2944 target = 0.037872 restraints weight = 15182.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.038369 restraints weight = 13071.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.2913
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5904  Z= 0.134
  Angle     :  0.555   8.898   8002  Z= 0.268
  Chirality :  0.041   0.171    887
  Planarity :  0.004   0.042    997
  Dihedral  : 12.743 105.714    925
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 7.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.99 (0.33), residues: 688
  helix:  2.31 (0.30), residues: 337
  sheet:  0.77 (0.43), residues: 132
  loop :  0.19 (0.43), residues: 219

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O1850 
 TYR   0.011   0.001   TYR O1117 
 PHE   0.021   0.001   PHE O1763 
 TRP   0.023   0.002   TRP O1840 
 HIS   0.002   0.001   HIS O1658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 5904)
  covalent geometry    : angle       0.55478 ( 8002)
  hydrogen bonds       : bond        0.02940 (  256)
  hydrogen bonds       : angle       4.20643 (  735)

*********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 90
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9312 (tpt) cc_final: 0.8870 (tpt)
REVERT: O 1157 MET cc_start: 0.8840 (mmm) cc_final: 0.8533 (mmm)
REVERT: O 1162 LEU cc_start: 0.9776 (mm) cc_final: 0.9479 (pp)
REVERT: O 1166 TRP cc_start: 0.9000 (t-100) cc_final: 0.8633 (t-100)
REVERT: O 1192 SER cc_start: 0.8766 (m) cc_final: 0.8229 (p)
REVERT: O 1195 TYR cc_start: 0.7939 (m-10) cc_final: 0.7716 (m-80)
REVERT: O 1288 MET cc_start: 0.9467 (mmp) cc_final: 0.9241 (mmm)
REVERT: O 1294 GLU cc_start: 0.9280 (mt-10) cc_final: 0.9055 (mt-10)
REVERT: O 1421 LEU cc_start: 0.9535 (tp) cc_final: 0.9215 (pp)
REVERT: O 1566 CYS cc_start: 0.9492 (m) cc_final: 0.8902 (p)
REVERT: O 1584 PHE cc_start: 0.9116 (m-80) cc_final: 0.8490 (m-80)
REVERT: O 1613 MET cc_start: 0.9548 (mtm) cc_final: 0.8175 (mtm)
REVERT: O 1657 MET cc_start: 0.8552 (mmp) cc_final: 0.8322 (mmp)
REVERT: O 1680 MET cc_start: 0.8324 (mmm) cc_final: 0.8035 (mmm)
REVERT: O 1760 ARG cc_start: 0.9632 (mtm110) cc_final: 0.9429 (mtm110)
REVERT: O 1776 ASP cc_start: 0.8607 (t0) cc_final: 0.8059 (m-30)
REVERT: O 1783 PHE cc_start: 0.9029 (t80) cc_final: 0.8267 (t80)
REVERT: O 1814 MET cc_start: 0.9513 (mtt) cc_final: 0.8974 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 90
  average time/residue: 0.1011
  time to fit residues: 11.3844
Evaluate side-chains
  73 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 8 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 10 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0980
   chunk 49 optimal weight:    9.9990
   chunk 50 optimal weight:    3.9990
   chunk 53 optimal weight:    4.9990
   chunk 24 optimal weight:    8.9990
   chunk 43 optimal weight:    1.9990
   chunk 63 optimal weight:    0.5980
   overall best weight:    1.9386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
O1241 HIS
O1309 GLN
** O1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3230 r_free = 0.3230 target = 0.046225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2749 r_free = 0.2749 target = 0.032270 restraints weight = 42195.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.033439 restraints weight = 26894.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.034239 restraints weight = 19784.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.2844 r_free = 0.2844 target = 0.034805 restraints weight = 15997.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2857 r_free = 0.2857 target = 0.035190 restraints weight = 13788.184|
|-----------------------------------------------------------------------------|
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5904  Z= 0.228
  Angle     :  0.633   7.979   8002  Z= 0.312
  Chirality :  0.041   0.188    887
  Planarity :  0.004   0.036    997
  Dihedral  : 12.849 109.581    925
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 12.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.05 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.78 (0.32), residues: 688
  helix:  2.16 (0.29), residues: 333
  sheet:  0.77 (0.43), residues: 132
  loop :  0.01 (0.41), residues: 223

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG O1266 
 TYR   0.022   0.001   TYR O1140 
 PHE   0.015   0.002   PHE O1777 
 TRP   0.015   0.002   TRP O1840 
 HIS   0.005   0.001   HIS O1241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00465 ( 5904)
  covalent geometry    : angle       0.63254 ( 8002)
  hydrogen bonds       : bond        0.03336 (  256)
  hydrogen bonds       : angle       4.50116 (  735)

*********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9302 (tpt) cc_final: 0.8846 (tpt)
REVERT: O 1157 MET cc_start: 0.8930 (mmm) cc_final: 0.8553 (mmm)
REVERT: O 1162 LEU cc_start: 0.9785 (mm) cc_final: 0.9440 (pp)
REVERT: O 1247 VAL cc_start: 0.9372 (t) cc_final: 0.8947 (p)
REVERT: O 1286 MET cc_start: 0.8352 (pmm) cc_final: 0.7552 (pmm)
REVERT: O 1288 MET cc_start: 0.9342 (mmp) cc_final: 0.9033 (mmm)
REVERT: O 1294 GLU cc_start: 0.9253 (mt-10) cc_final: 0.9031 (mt-10)
REVERT: O 1566 CYS cc_start: 0.9546 (m) cc_final: 0.8984 (p)
REVERT: O 1584 PHE cc_start: 0.9420 (m-80) cc_final: 0.8835 (m-80)
REVERT: O 1613 MET cc_start: 0.9633 (mtm) cc_final: 0.8604 (mtm)
REVERT: O 1638 LEU cc_start: 0.9759 (tp) cc_final: 0.9420 (mt)
REVERT: O 1642 MET cc_start: 0.8784 (mmm) cc_final: 0.8514 (mmm)
REVERT: O 1776 ASP cc_start: 0.8809 (t0) cc_final: 0.8187 (m-30)
REVERT: O 1783 PHE cc_start: 0.9168 (t80) cc_final: 0.8582 (t80)
REVERT: O 1814 MET cc_start: 0.9629 (mtt) cc_final: 0.8871 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.0920
  time to fit residues: 9.0894
Evaluate side-chains
  56 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0980
   chunk 62 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 26 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 22 optimal weight:    3.9990
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** O1636 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** O1757 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.047368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.033435 restraints weight = 40715.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.034617 restraints weight = 26151.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.2875 r_free = 0.2875 target = 0.035488 restraints weight = 19210.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.036019 restraints weight = 15354.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2909 r_free = 0.2909 target = 0.036479 restraints weight = 13251.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.2866
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8160
moved from start:          0.3659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   5904  Z= 0.113
  Angle     :  0.542   7.884   8002  Z= 0.263
  Chirality :  0.040   0.179    887
  Planarity :  0.004   0.034    997
  Dihedral  : 12.815 111.702    925
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.79 (0.33), residues: 688
  helix:  2.02 (0.29), residues: 341
  sheet:  0.83 (0.44), residues: 132
  loop :  0.17 (0.43), residues: 215

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O1850 
 TYR   0.012   0.001   TYR O1140 
 PHE   0.007   0.001   PHE O1733 
 TRP   0.007   0.001   TRP O1840 
 HIS   0.002   0.001   HIS O1658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00243 ( 5904)
  covalent geometry    : angle       0.54205 ( 8002)
  hydrogen bonds       : bond        0.02732 (  256)
  hydrogen bonds       : angle       4.43172 (  735)

*********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  75 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.200 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9323 (tpt) cc_final: 0.8881 (tpt)
REVERT: O 1157 MET cc_start: 0.8998 (mmm) cc_final: 0.8596 (mmm)
REVERT: O 1162 LEU cc_start: 0.9774 (mm) cc_final: 0.9403 (pp)
REVERT: O 1175 ARG cc_start: 0.8843 (tpp80) cc_final: 0.8537 (mmt90)
REVERT: O 1247 VAL cc_start: 0.9391 (t) cc_final: 0.9017 (p)
REVERT: O 1286 MET cc_start: 0.8301 (pmm) cc_final: 0.7473 (pmm)
REVERT: O 1294 GLU cc_start: 0.9245 (mt-10) cc_final: 0.9020 (mt-10)
REVERT: O 1566 CYS cc_start: 0.9498 (m) cc_final: 0.8937 (p)
REVERT: O 1584 PHE cc_start: 0.9386 (m-80) cc_final: 0.8745 (m-80)
REVERT: O 1613 MET cc_start: 0.9638 (mtm) cc_final: 0.8449 (mtm)
REVERT: O 1633 LYS cc_start: 0.9571 (mttt) cc_final: 0.9364 (mtpt)
REVERT: O 1776 ASP cc_start: 0.8830 (t0) cc_final: 0.8203 (m-30)
REVERT: O 1783 PHE cc_start: 0.9112 (t80) cc_final: 0.8456 (t80)
REVERT: O 1814 MET cc_start: 0.9587 (mtt) cc_final: 0.8907 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.0847
  time to fit residues: 8.0924
Evaluate side-chains
  65 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 63 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 55 optimal weight:    0.2980
   chunk 52 optimal weight:    5.9990
   chunk 4 optimal weight:    4.9990
   chunk 11 optimal weight:    4.9990
   chunk 59 optimal weight:    0.9980
   chunk 30 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
O1636 GLN
** O1815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.047072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.033102 restraints weight = 42268.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2831 r_free = 0.2831 target = 0.034325 restraints weight = 26497.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2860 r_free = 0.2860 target = 0.035179 restraints weight = 19385.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2879 r_free = 0.2879 target = 0.035729 restraints weight = 15574.542|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.2891 r_free = 0.2891 target = 0.036076 restraints weight = 13443.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.2845
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.3890

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5904  Z= 0.128
  Angle     :  0.535   7.695   8002  Z= 0.259
  Chirality :  0.040   0.180    887
  Planarity :  0.003   0.033    997
  Dihedral  : 12.813 113.458    925
  Min Nonbonded Distance : 2.055

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.81 %
    Favored  : 99.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.69 (0.32), residues: 688
  helix:  1.93 (0.29), residues: 340
  sheet:  0.82 (0.43), residues: 130
  loop :  0.12 (0.42), residues: 218

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG O1266 
 TYR   0.011   0.001   TYR O1140 
 PHE   0.010   0.001   PHE O1669 
 TRP   0.033   0.002   TRP O1826 
 HIS   0.002   0.001   HIS O1689 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 5904)
  covalent geometry    : angle       0.53542 ( 8002)
  hydrogen bonds       : bond        0.02647 (  256)
  hydrogen bonds       : angle       4.40582 (  735)

*********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.249 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9300 (tpt) cc_final: 0.8844 (tpt)
REVERT: O 1157 MET cc_start: 0.8823 (mmm) cc_final: 0.8589 (mmm)
REVERT: O 1162 LEU cc_start: 0.9764 (mm) cc_final: 0.9399 (pp)
REVERT: O 1234 ASP cc_start: 0.9375 (m-30) cc_final: 0.9123 (p0)
REVERT: O 1247 VAL cc_start: 0.9336 (t) cc_final: 0.9014 (p)
REVERT: O 1282 CYS cc_start: 0.9487 (m) cc_final: 0.9065 (m)
REVERT: O 1286 MET cc_start: 0.8393 (pmm) cc_final: 0.7500 (pmm)
REVERT: O 1566 CYS cc_start: 0.9455 (m) cc_final: 0.8919 (p)
REVERT: O 1584 PHE cc_start: 0.9370 (m-80) cc_final: 0.8714 (m-80)
REVERT: O 1613 MET cc_start: 0.9609 (mtm) cc_final: 0.8360 (mtm)
REVERT: O 1638 LEU cc_start: 0.9709 (tp) cc_final: 0.9441 (mt)
REVERT: O 1642 MET cc_start: 0.8660 (mmm) cc_final: 0.8429 (mmm)
REVERT: O 1680 MET cc_start: 0.8159 (mmm) cc_final: 0.7835 (mmm)
REVERT: O 1776 ASP cc_start: 0.8877 (t0) cc_final: 0.8237 (m-30)
REVERT: O 1783 PHE cc_start: 0.9092 (t80) cc_final: 0.8423 (t80)
REVERT: O 1814 MET cc_start: 0.9495 (mtt) cc_final: 0.8946 (mmm)
REVERT: O 1840 TRP cc_start: 0.9164 (m100) cc_final: 0.8434 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.0829
  time to fit residues: 7.9671
Evaluate side-chains
  58 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 30 optimal weight:    4.9990
   chunk 60 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0980
   chunk 54 optimal weight:    0.9990
   chunk 44 optimal weight:    0.7980
   chunk 36 optimal weight:    9.9990
   chunk 41 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 35 optimal weight:    8.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
** O1815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.047015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.2793 r_free = 0.2793 target = 0.033054 restraints weight = 42116.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2835 r_free = 0.2835 target = 0.034235 restraints weight = 26985.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.035099 restraints weight = 19901.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.2885 r_free = 0.2885 target = 0.035676 restraints weight = 16032.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2898 r_free = 0.2898 target = 0.036052 restraints weight = 13770.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8213
moved from start:          0.4054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5904  Z= 0.122
  Angle     :  0.565  11.640   8002  Z= 0.275
  Chirality :  0.041   0.180    887
  Planarity :  0.004   0.043    997
  Dihedral  : 12.846 115.691    925
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.71 (0.33), residues: 688
  helix:  1.91 (0.29), residues: 344
  sheet:  0.87 (0.44), residues: 130
  loop :  0.12 (0.43), residues: 214

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O1266 
 TYR   0.010   0.001   TYR O1140 
 PHE   0.007   0.001   PHE O1763 
 TRP   0.040   0.002   TRP O1826 
 HIS   0.003   0.001   HIS O1268 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 5904)
  covalent geometry    : angle       0.56486 ( 8002)
  hydrogen bonds       : bond        0.02669 (  256)
  hydrogen bonds       : angle       4.31017 (  735)

*********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.276 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9267 (tpt) cc_final: 0.8808 (tpt)
REVERT: O 1157 MET cc_start: 0.8836 (mmm) cc_final: 0.8537 (mmm)
REVERT: O 1162 LEU cc_start: 0.9732 (mm) cc_final: 0.9373 (pp)
REVERT: O 1247 VAL cc_start: 0.9337 (t) cc_final: 0.8951 (p)
REVERT: O 1282 CYS cc_start: 0.9457 (m) cc_final: 0.9038 (m)
REVERT: O 1286 MET cc_start: 0.8410 (pmm) cc_final: 0.7457 (pmm)
REVERT: O 1566 CYS cc_start: 0.9378 (m) cc_final: 0.8878 (p)
REVERT: O 1584 PHE cc_start: 0.9323 (m-80) cc_final: 0.8668 (m-80)
REVERT: O 1613 MET cc_start: 0.9558 (mtm) cc_final: 0.8250 (mtm)
REVERT: O 1642 MET cc_start: 0.8712 (mmm) cc_final: 0.8439 (mmm)
REVERT: O 1680 MET cc_start: 0.8140 (mmm) cc_final: 0.7697 (mmm)
REVERT: O 1776 ASP cc_start: 0.8920 (t0) cc_final: 0.8254 (m-30)
REVERT: O 1783 PHE cc_start: 0.9029 (t80) cc_final: 0.8333 (t80)
REVERT: O 1814 MET cc_start: 0.9473 (mtt) cc_final: 0.8949 (mmm)
REVERT: O 1840 TRP cc_start: 0.9104 (m100) cc_final: 0.8396 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 71
  average time/residue: 0.0786
  time to fit residues: 7.5608
Evaluate side-chains
  59 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 68 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 59 optimal weight:    2.9990
   chunk 35 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 36 optimal weight:    3.9990
   chunk 34 optimal weight:    1.9990
   overall best weight:    1.9588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
O1645 ASN
** O1815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.045084 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2721 r_free = 0.2721 target = 0.031322 restraints weight = 43381.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.032424 restraints weight = 27646.926|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.2790 r_free = 0.2790 target = 0.033210 restraints weight = 20446.156|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.033637 restraints weight = 16596.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.2819 r_free = 0.2819 target = 0.034020 restraints weight = 14587.631|
|-----------------------------------------------------------------------------|
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8288
moved from start:          0.4401

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   5904  Z= 0.220
  Angle     :  0.643  10.783   8002  Z= 0.321
  Chirality :  0.041   0.187    887
  Planarity :  0.004   0.037    997
  Dihedral  : 13.037 119.178    925
  Min Nonbonded Distance : 2.007

Molprobity Statistics.
  All-atom Clashscore : 13.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.51 (0.33), residues: 688
  helix:  1.76 (0.29), residues: 345
  sheet:  0.74 (0.44), residues: 132
  loop :  0.03 (0.42), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG O1422 
 TYR   0.012   0.001   TYR O1140 
 PHE   0.010   0.002   PHE O1763 
 TRP   0.015   0.002   TRP O1826 
 HIS   0.004   0.001   HIS O1689 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 5904)
  covalent geometry    : angle       0.64303 ( 8002)
  hydrogen bonds       : bond        0.03195 (  256)
  hydrogen bonds       : angle       4.78449 (  735)

*********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9280 (tpt) cc_final: 0.8694 (tpt)
REVERT: O 1157 MET cc_start: 0.8858 (mmm) cc_final: 0.8570 (mmm)
REVERT: O 1162 LEU cc_start: 0.9753 (mm) cc_final: 0.9400 (pp)
REVERT: O 1247 VAL cc_start: 0.9337 (t) cc_final: 0.8950 (p)
REVERT: O 1282 CYS cc_start: 0.9435 (m) cc_final: 0.9047 (m)
REVERT: O 1286 MET cc_start: 0.8447 (pmm) cc_final: 0.7435 (pmm)
REVERT: O 1566 CYS cc_start: 0.9427 (m) cc_final: 0.8894 (p)
REVERT: O 1584 PHE cc_start: 0.9456 (m-80) cc_final: 0.8895 (m-80)
REVERT: O 1613 MET cc_start: 0.9565 (mtm) cc_final: 0.8905 (mtm)
REVERT: O 1756 MET cc_start: 0.9618 (tmm) cc_final: 0.9388 (tmm)
REVERT: O 1776 ASP cc_start: 0.9032 (t0) cc_final: 0.8333 (m-30)
REVERT: O 1783 PHE cc_start: 0.9082 (t80) cc_final: 0.8367 (t80)
REVERT: O 1814 MET cc_start: 0.9548 (mtt) cc_final: 0.8999 (mmm)
REVERT: O 1840 TRP cc_start: 0.9211 (m100) cc_final: 0.8532 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.0820
  time to fit residues: 7.3973
Evaluate side-chains
  54 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 22 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 50 optimal weight:    0.0570
   chunk 60 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 38 optimal weight:    0.8980
   overall best weight:    0.7498

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.045870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2756 r_free = 0.2756 target = 0.032175 restraints weight = 42798.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2798 r_free = 0.2798 target = 0.033342 restraints weight = 27269.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2826 r_free = 0.2826 target = 0.034160 restraints weight = 20007.051|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.034705 restraints weight = 16111.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.035045 restraints weight = 13893.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8235
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5904  Z= 0.124
  Angle     :  0.615  13.748   8002  Z= 0.302
  Chirality :  0.042   0.183    887
  Planarity :  0.003   0.034    997
  Dihedral  : 12.961 119.642    925
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.65 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.53 (0.33), residues: 688
  helix:  1.76 (0.29), residues: 344
  sheet:  0.65 (0.43), residues: 133
  loop :  0.14 (0.43), residues: 211

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O1266 
 TYR   0.010   0.001   TYR O1140 
 PHE   0.006   0.001   PHE O1194 
 TRP   0.019   0.002   TRP O1826 
 HIS   0.002   0.001   HIS O1689 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 5904)
  covalent geometry    : angle       0.61514 ( 8002)
  hydrogen bonds       : bond        0.02886 (  256)
  hydrogen bonds       : angle       4.61567 (  735)

*********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  68 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9285 (tpt) cc_final: 0.8865 (tpt)
REVERT: O 1157 MET cc_start: 0.8886 (mmm) cc_final: 0.8602 (mmm)
REVERT: O 1162 LEU cc_start: 0.9749 (mm) cc_final: 0.9416 (pp)
REVERT: O 1247 VAL cc_start: 0.9308 (t) cc_final: 0.8926 (p)
REVERT: O 1282 CYS cc_start: 0.9483 (m) cc_final: 0.9097 (m)
REVERT: O 1286 MET cc_start: 0.8433 (pmm) cc_final: 0.7463 (pmm)
REVERT: O 1566 CYS cc_start: 0.9384 (m) cc_final: 0.8866 (p)
REVERT: O 1584 PHE cc_start: 0.9421 (m-80) cc_final: 0.8828 (m-80)
REVERT: O 1613 MET cc_start: 0.9568 (mtm) cc_final: 0.9083 (mtp)
REVERT: O 1760 ARG cc_start: 0.9613 (mtm110) cc_final: 0.9384 (mtm110)
REVERT: O 1776 ASP cc_start: 0.9058 (t0) cc_final: 0.8367 (m-30)
REVERT: O 1783 PHE cc_start: 0.8992 (t80) cc_final: 0.8281 (t80)
REVERT: O 1814 MET cc_start: 0.9511 (mtt) cc_final: 0.8982 (mmm)
REVERT: O 1840 TRP cc_start: 0.9133 (m100) cc_final: 0.8447 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.0917
  time to fit residues: 8.1712
Evaluate side-chains
  57 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 57
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 25 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    0.7980
   chunk 39 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 51 optimal weight:    2.9990
   chunk 68 optimal weight:    0.1980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.046038 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.032206 restraints weight = 42998.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.033382 restraints weight = 27363.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.034187 restraints weight = 20048.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2855 r_free = 0.2855 target = 0.034797 restraints weight = 16109.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.035172 restraints weight = 13828.141|
|-----------------------------------------------------------------------------|
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8245
moved from start:          0.4546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5904  Z= 0.125
  Angle     :  0.622  14.206   8002  Z= 0.308
  Chirality :  0.042   0.183    887
  Planarity :  0.003   0.033    997
  Dihedral  : 12.943 119.365    925
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 11.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.32 %
    Favored  : 99.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.33), residues: 688
  helix:  1.66 (0.29), residues: 344
  sheet:  0.70 (0.43), residues: 132
  loop :  0.05 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O1850 
 TYR   0.016   0.001   TYR O1195 
 PHE   0.008   0.001   PHE O1763 
 TRP   0.018   0.002   TRP O1826 
 HIS   0.002   0.001   HIS O1265 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 5904)
  covalent geometry    : angle       0.62177 ( 8002)
  hydrogen bonds       : bond        0.02996 (  256)
  hydrogen bonds       : angle       4.58919 (  735)

********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************

-------------------------------------------------------------------------------
Update Rama plot phi/psi targets (oldfield only)
************************************************

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1376 Ramachandran restraints generated.
    688 Oldfield, 0 Emsley, 688 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: O 1105 MET cc_start: 0.9269 (tpt) cc_final: 0.8846 (tpt)
REVERT: O 1162 LEU cc_start: 0.9750 (mm) cc_final: 0.9399 (pp)
REVERT: O 1247 VAL cc_start: 0.9292 (t) cc_final: 0.8928 (p)
REVERT: O 1282 CYS cc_start: 0.9431 (m) cc_final: 0.9011 (m)
REVERT: O 1566 CYS cc_start: 0.9357 (m) cc_final: 0.8865 (p)
REVERT: O 1582 ILE cc_start: 0.8987 (pt) cc_final: 0.8777 (pt)
REVERT: O 1584 PHE cc_start: 0.9391 (m-80) cc_final: 0.8798 (m-80)
REVERT: O 1613 MET cc_start: 0.9530 (mtm) cc_final: 0.9045 (mtp)
REVERT: O 1756 MET cc_start: 0.9514 (tmm) cc_final: 0.9291 (tmm)
REVERT: O 1759 MET cc_start: 0.9636 (mmp) cc_final: 0.9195 (mmm)
REVERT: O 1760 ARG cc_start: 0.9609 (mtm110) cc_final: 0.9380 (mtm110)
REVERT: O 1776 ASP cc_start: 0.9091 (t0) cc_final: 0.8383 (m-30)
REVERT: O 1783 PHE cc_start: 0.8975 (t80) cc_final: 0.8254 (t80)
REVERT: O 1814 MET cc_start: 0.9482 (mtt) cc_final: 0.8897 (mmm)
REVERT: O 1840 TRP cc_start: 0.9098 (m100) cc_final: 0.8437 (m100)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.0858
  time to fit residues: 7.8180
Evaluate side-chains
  58 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 58
  time to evaluate  : 0.307 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 69
   random chunks:
   chunk 37 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 24 optimal weight:    0.6980
   chunk 68 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 61 optimal weight:    3.9990
   chunk 57 optimal weight:    0.6980
   chunk 22 optimal weight:    7.9990
   chunk 60 optimal weight:    0.0980
   chunk 58 optimal weight:    2.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...

Flipped N/Q/H residues before XYZ refinement:
O1267 ASN
** O1815 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.045610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2736 r_free = 0.2736 target = 0.031645 restraints weight = 42388.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2779 r_free = 0.2779 target = 0.032784 restraints weight = 27532.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2805 r_free = 0.2805 target = 0.033526 restraints weight = 20367.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.2827 r_free = 0.2827 target = 0.034124 restraints weight = 16584.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.2840 r_free = 0.2840 target = 0.034492 restraints weight = 14304.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.2805
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.4733

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5904  Z= 0.150
  Angle     :  0.634  13.339   8002  Z= 0.314
  Chirality :  0.041   0.180    887
  Planarity :  0.004   0.034    997
  Dihedral  : 13.051 118.389    925
  Min Nonbonded Distance : 1.929

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.33), residues: 688
  helix:  1.56 (0.29), residues: 344
  sheet:  0.65 (0.43), residues: 132
  loop :  0.10 (0.43), residues: 212

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG O1175 
 TYR   0.010   0.001   TYR O1195 
 PHE   0.009   0.001   PHE O1763 
 TRP   0.012   0.002   TRP O1826 
 HIS   0.002   0.001   HIS O1689 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 5904)
  covalent geometry    : angle       0.63409 ( 8002)
  hydrogen bonds       : bond        0.03007 (  256)
  hydrogen bonds       : angle       4.58671 (  735)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1141.63 seconds
wall clock time: 20 minutes 31.26 seconds (1231.26 seconds total)